rs3956418

Variant names:

• chr1-83363674-G-A
• rs3956418
• ENST00000715927.1:n.227-50361C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715927.1(LINC01725):​n.227-50361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,012 control chromosomes in the GnomAD database, including 34,973 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34973 hom., cov: 33)
• Consequence: LINC01725 ENST00000715927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.672
• Publications: 2 publications found

Genes affected

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000715927.1	n.227-50361C>T		intron_variant	Intron 2 of 2
LINC01725	ENST00000715928.1	n.396-1420C>T		intron_variant	Intron 5 of 5
LINC01725	ENST00000715929.1	n.284-1420C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102158 AN: 151894 Hom.: 34923 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.642

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.673 AC: 102264 AN: 152012 Hom.: 34973 Cov.: 33 AF XY: 0.673 AC XY: 50042 AN XY: 74318

African (AFR) AF: 0.786 AC: 32595 AN: 41478

American (AMR) AF: 0.613 AC: 9343 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.837 AC: 4326 AN: 5170

South Asian (SAS) AF: 0.668 AC: 3226 AN: 4832

European-Finnish (FIN) AF: 0.569 AC: 6019 AN: 10576

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42571 AN: 67922

Other (OTH) AF: 0.642 AC: 1355 AN: 2110

Alfa AF: 0.647 Hom.: 25575

Bravo AF: 0.679

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.58
PhyloP100		0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3956418; hg19: chr1-83829357;